Getting help with R

class: title-slide, nobar
![:img right: 25px, bottom: 25px, 50%, , ](figures/R.png)

## Workshop: Dealing with Data in R
# Getting help in R
## After this workshop

.footnote[Steffi LaZerte <https://steffilazerte.ca> | *Compiled: 2022-01-26*]

---
class: section

# First things first

Save previous script

Open New File <br>.medium[(make sure you're in the RStudio Project)]

![:spacer 10px]()

Add `library(tidyverse)` to the top

Save this new script

.medium[consider names like `troubleshoting.R` or `5_getting_help.R`]

---
class: nobar
![:img center, bottom: 0, 100%, ,](https://pbs.twimg.com/media/EK8s79kUEAU3cAT?format=jpg&name=4096x4096)

.footnote[Artwork by [@allison_horst on Twitter](https://twitter.com/allison_horst/status/1202229050284003328/photo/1) -- *"Knowing so little never felt so fun. #rstats"*]

---
class: section

# Troubleshooting

---
# Bit by bit

### Line by line

- R is sequential
- If you skip lines, you're not running that part

```r
#library(tidyverse)
count(mtcars, am)
```

```
## Error in count(mtcars, am): could not find function "count"
```

--
- Error? Start at the beginning and go line by line

```r
library(tidyverse)
count(mtcars, am)
```

```
##   am  n
## 1  0 19
## 2  1 13
```

---
# Bit by bit

### Line by line

```r
# Load Data
size <- read_csv("./data/grain_size2.csv")

# First modification
size <- mutate(size, 
               total_sand = coarse_sand + medium_sand + fine_sand,
               total_silt = coarse_silt + medium_silt + fine_silt)

# Second modification
size <- size %>%
  group_by(plot) %>%
  summarize(n = n(),
            total_sand = sum(total_sand),
            mean_sand = mean(total_sand),
            sd_sand = sd(total_sand),
            se_sand = sd_sand / sqrt(n))
```

![:box 40%, 15%, 50%](Especially important if loading and modifying data)
![:box 25%, 60%, 30%](Can't run 1st modification<br>after 2nd modification)

---
# Bit by bit
### Section by section

```r
size <- read_csv("./data/grain_size2.csv") %>%
  mutate(total_sand = coarse_sand + medium_sand + fine_sand,
         total_silt = coarse_silt + medium_silt + fine_silt) %>%
  group_by(plot) %>%
  summarize(n = n(),
            total_sand = sum(total_sand),
            mean_sand = mean(totall_sand),
            sd_sand = sd(total_sand),
            se_sand = sd_sand / sqrt(n))
```

```
## Error: Problem with `summarise()` column `mean_sand`.
## ℹ `mean_sand = mean(totall_sand)`.
## x object 'totall_sand' not found
## ℹ The error occurred in group 1: plot = "CSP01".
```

---
# Bit by bit
### Section by section

```r
size <- read_csv("./data/grain_size2.csv")
```

No error

```r
size <- read_csv("./data/grain_size2.csv") %>%
  mutate(total_sand = coarse_sand + medium_sand + fine_sand,
         total_silt = coarse_silt + medium_silt + fine_silt)
```

No error

```r
size <- read_csv("./data/grain_size2.csv") %>%
  mutate(total_sand = coarse_sand + medium_sand + fine_sand,
         total_silt = coarse_silt + medium_silt + fine_silt) %>%
  group_by(plot) 
```

No error

---
# Bit by bit
### Section by section

```
## Error: Problem with `summarise()` column `mean_sand`.
## ℹ `mean_sand = mean(totall_sand)`.
## x object 'totall_sand' not found
## ℹ The error occurred in group 1: plot = "CSP01".
```

Ah ha!

---
# Bit by bit

## Applies to error messages too

- First, don't panic!
- Look at the error bit by bit

```
## Error: Problem with `summarise()` column `mean_sand`.
## ℹ `mean_sand = mean(totall_sand)`.
## x object 'totall_sand' not found
## ℹ The error occurred in group 1: plot = "CSP01".
```

---
# Bit by bit

## Applies to error messages too

```
Error: Problem with 'summarise()' column 'mean_sand'`
```
Okay, we know the problem is in the `summarize()` part and then `mean_sand` part of that

![:spacer 10px]()

```
ℹ 'mean_sand = mean(totall_sand)'
x object 'totall_sand' not found
```
Looks like this is the line with the problem.   
And the problem is `object 'totall_sand' not found`. **Ooops! Typo!**

![:spacer 10px]()

```
ℹ The error occurred in group 1: plot = "CSP01".
```
Lastly, it's telling us that the problem was when working with this group of data. 
(This can be useful when troubleshooting, because you can `filter()` your data and take a look)

---
class: nobar

![:img center, bottom: 0, 90%, ,](https://raw.githubusercontent.com/allisonhorst/stats-illustrations/master/other-stats-artwork/debugging.jpg)

.footnote[Artwork by [@allison_horst](https://github.com/allisonhorst/stats-illustrations)]

---
class: section

# R is never wrong

![:spacer 32px]()

---
class: section

# R is never wrong

## Just sometimes unhelpful!

---
class: section

# Getting Help

---
# Cheat Sheets

### RStudio Menu

- Help
  - Cheatsheets

![:spacer 15px]()

> Take a look yourself

![:img right: 0, bottom: 15px, 73%, , ](figures/ggplot.png)

---
# Vignettes

Many packages come with vignettes (aka, R tutorials)

### List Vignettes

```r
vignette(package = "ggplot2")
```

```
Vignettes in package ‘ggplot2’:

ggplot2-specs                      Aesthetic specifications (source, html)
extending-ggplot2                  Extending ggplot2 (source, html)
profiling                          Profiling Performance (source, html)
```

### Load Vignettes

```r
vignette("ggplot2-specs", package = "ggplot2")
```

> Try it!

---
# Tutorials

### Vignettes also online
- e.g., [`tidyverse`](https://tidyverse.org)

### Organizations/Websites
- [Software Carpentry](https://software-carpentry.org/)
- [STHDA](http://www.sthda.com/english/)

![:img right: 25px, bottom: 75px, 65%, , ggplot2 website](figures/tidyverse_ggplot2.png)

---
# Books!

### Free Online
- [R for Data Science](http://r4ds.had.co.nz/data-visualisation.html) (read it!)
- [R Graphics Cookbook](https://r-graphics.org/) (how to do X)
- [`ggplot2`](https://ggplot2-book.org/) (next level)
- [Data Visualization: A practical introduction](http://socviz.co/)
- [Geocomputation with R](https://bookdown.org/robinlovelace/geocompr/) (spatial, GIS, maps)
- [Statistical Inference via Data Science: A ModernDive into R and the tidyverse](https://moderndive.com) (stats)

---
class: section

# Specific help

---
# Examples

### In R

```r
?geom_boxplot
```

> Copy and paste the examples into your console

---
class: split-50
# Examples

.columnl[
### On the web

- Nice to see expected output
- Helps figure out if it's your system or your code
]
![:img right: 0, bottom: 0, 51.5%, , ](figures/ggplot_examples.png)

---
class: space-list
# Web searches

- **Always include "R" in the search**
- **Include the package name!**
- **Use keywords**
- **Some errors are very general**

---
class: space-list
# Web searches

- **Always include "R" in the search**
- **Include the package name!**
  - .hl[Try "R boxplots" vs. "R boxplots ggplot2"]
- **Use keywords**
  - .hl[Try "R boxplots ggplot2 notch"]
- **Some errors are very general**
  - .hl[Try "R Error: object 'm' not found"]

---
class: section
# Stackoverflow etc.

### ["R how to remove duplicate rows"](https://stackoverflow.com/questions/13967063/remove-duplicated-rows)

---
class: space-list
# Stackoverflow etc.

### Things to consider

- Date (i.e., R version, Package Version)
- Packages used (`tidyverse`? R base? A mix?)
- What are the example data? 
  - `mtcars` and `iris` are commonly used data sets built into R base
  - `msleep` and `diamonds` are commonly used data sets built into `ggplot2`
- What are the example columns?
- What is actually required to answer *your* question?

---
# Asking for Help

### Not useful

- "I got an error"
- "It didn't work"

### Better!

- "I got *this* error"
- "It didn't give me *this*"

### Best!!

- "I did *this* and I got *this* error"
- "I expected it to do *this*, but in fact the output was *this*"

### Best of the Best!!!

- "I did *this* [small reproducible code, including data set] and I got *this* [exact error/output]"

---
class: space-list
# Reproducible Examples

.columnl[
- Minimal code and data required to reproduce the error
- Often preparing this actually helps you solve the error!
- Includes
  - packages (`library()`)
  - data
  - runnable code
]

---
# Reproducible Examples

## How do I change the order of `vore`?

.columnl[
### Not reproducible

```r
ggplot(data = m, aes(x = vore, y = awake, fill = `Body Size`)) +
  theme_bw() + 
  theme(axis.title.x = element_blank()) +
  geom_boxplot() +
  scale_fill_viridis_d() +
  labs(y = "Awake time (hrs)",
       title = "Awake time by Diet")
```

```
## Error in ggplot(data = m, aes(x = vore, y = awake, fill = `Body Size`)): could not find function "ggplot"
```

- No indication of packages
- No indication of what `m` is

]

---
class: split-60
# Reproducible Examples

## How do I change the order of `vore`?

.columnl[
### Reproducible, but not minimal

```r
*library(ggplot2)

*m <- msleep %>%
* mutate(`Body Size` = if_else(bodywt > median(bodywt),
*                              "Large", "Small"))

ggplot(m, aes(x = vore, y = awake, fill = `Body Size`)) +
  theme_bw() + 
  theme(axis.title.x = element_blank()) +
  geom_boxplot() +
  scale_fill_viridis_d() +
  labs(y = "Awake time (hrs)",
       title = "Awake time by Diet")
```
]

.columnr[
![:img right: 15px, bottom 50px, 40%, , ](5_getting_help_files/figure-html/not_minimal-1.png)
]

---
class: split-60
# Reproducible Examples

## How do I change the order of `vore`?

.columnl[

### Reproducible AND Minimal

```r
library(ggplot2)

ggplot(msleep, aes(x = vore, y = awake)) +
  geom_boxplot()
```
]
.columnr[
![:img right: 15px, bottom 50px, 40%, , ](5_getting_help_files/figure-html/minimal-1.png)
]

---
class: section

# Paying it forward

---
# Citing Software

### In-line Text
- Software name
- Version
- Programmers/authors OR Journal article releasing the software (if available)

### Bibliography
- Journal article releasing the program **OR**
- Programmers/authors
- Year of release
- Program Name
- URL

---
# Citing R

### Inline

"All statistical analyses were performed with R statistical software (v3.6.2, R Core Team 2019)."

### Bibliography

.hanging[
R Core Team (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.]

---
# Citing R

### Version information

```r
R.Version()$version.string
```

```
## [1] "R version 4.1.2 (2021-11-01)"
```

### Citation information

```r
citation()
```

```
## 
## To cite R in publications use:
## 
##   R Core Team (2021). R: A language and environment for statistical
##   computing. R Foundation for Statistical Computing, Vienna, Austria.
##   URL https://www.R-project.org/.
```

---
# Citing R Packages

### Inline

"All statistical analyses were performed with R statistical software (v4.0.3, R Core Team 2020). We performed Type III ANOVAs using the 'car' package for R (v3.0.10, Fox and Weisberg)."

### Bibliography

.hanging[
John Fox and Sanford Weisberg (2019). An R Companion to Applied Regression, Third Edition. Thousand Oaks CA: Sage.]

---
# Citing R Packages

### Version information

```r
packageVersion("car")
```

```
## [1] '3.0.12'
```

### Citation information

```r
citation("car")
```

```
## 
## To cite the car package in publications use:
## 
##   John Fox and Sanford Weisberg (2019). An {R} Companion to Applied
##   Regression, Third Edition. Thousand Oaks CA: Sage. URL:
##   https://socialsciences.mcmaster.ca/jfox/Books/Companion/
```

![:spacer 10px]()

See more about citing packages in my rOpenSci blog post: [How to Cite R and R packages](https://ropensci.org/blog/2021/11/16/how-to-cite-r-and-r-packages/)

---
class: nobar
![:img center, bottom: 0, 53%, ,](https://github.com/allisonhorst/stats-illustrations/raw/master/rstats-artwork/r_first_then.png)

.footnote[Artwork by [@allison_horst](https://github.com/allisonhorst/stats-illustrations)]

![:spacer 100px]()

### You made it!

### Thank you!